The situation:
I am piloting a YV-666 (not my ship). I entered my own docked ship aboard the 666, a YT 1210, to install the locks while leaving a droid to pilot the 666. No problem.

First I had problem with the lock installs taking days instead of hours. That seems ok now. Then I could not leave my 1210. I got a bug message when trying to leave the room I was in. This to has gone away as of this AM and appears to be working now.

My problem is that when the 666 droped out of hyper I was stuck inside the docked 1210. I did not recieve any XP's for the trip.

I believe it only rewards XP if the assigned pilot is on board the flying entity. This is to prevent (back when you could drop out of a moving ship) flying a ship, hopping out and starting a bunch of them to get lots of XP quickly.

Ah was 6 hours away from the end of a 14 day Hyper-trip when the commander removed me as the pilot (the owner had had been arrested and the commander was 'securing' their assets), they did end up re-assigning me (about 4 minutes after ah logged out) but ah don't know if that would have made any difference by going back into the Cockpit

Ah understand the Exp is gone, but maybe could change it somewhere so no-one else has to waste 2weeks (was just 6 hours away from the end of the journey :()

Depends on when you logged out. XP when travelling is given to the assigned pilot that is inside that entity. And not in a docked entity, but so that your position says you are in that entity. Doesn't matter who started travel, when the pilot was assigned. All that matters is the pilot at the end of the journey.